When It Ends
by kmylove
Summary: What happens when things aren't what they seem to be? A red pill surrounded by mystery, a ship commander with a secret: is it just this or is it more? Chapter three uploaded. Reviwes are very welcome
1. Would You Mind

_This fanfiction has had many sources of inspiration. First of, there was an RPG plot that got developed on my forum, for which I have to thank parmazano, also known as Agent Smith or The Merovingian, and Not The One. Then I heard Within Temptation's song "What Have You Done", which allowed me to further develop the idea._

_The first chapter is vague, but I hope it is enjoyed. _

_**Disclaimer: I don't own any of the original trilogy characters. The lyrics used in this fiction are from the song "What Have You Done" performed by Within Temptation and belong to their respectful author.**_**  
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**Chapter 1: Would you mind if I killed you?**

_Would you mind if I killed you  
Would you mind if I tried to  
Cause you have turned into my worst enemy  
You carry hate that I feel  
It's over now_

A flash of lightning was enough for them to see each other, though for a brief second. They saw their true selves, their old selves, the distant memories that still bound them together but at the same moment separated them. But the past had to be left behind, they had to face the new reality where fate had cast them, a reality where they were each other's worst enemy, where they couldn't both live, where the death of one decided the fate of mankind.

If that lightning would have lasted longer, what would have they seen? They would have seen two motionless persons, standing in front of each other too far for them to see each other well in the deep darkness of the night, but closer than enemies would ever stand. None dared speak, none dared move.

One of them remembered the past and didn't want to let go, the other had vague memories of the past but couldn't feel connected to them in any way. One's eyes were still burning with the past and present love, the other's were steel cold and emotionless.

What did they wait for? One waited for a miracle which would never come, the other waited for the proper moment to attack.

Another flash of lightning... Their eyes spoke instead of their voices, agreeing that it was time, that it made no sense to still delay the moment...

They moved towards each other...


	2. It's Over Now

_Here is my second chapter. It took me more than I expected to write it, but I was really blocked at finding a name for the character and I kind of became rusty, it's been around a year since I last wrote anything, I need to get accustomed to it once more._

_Creditations and disclaimers are the same as for the first chapter._

_Enjoy reading and don't hesitate to comment._

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**Chapter 2: It's Over Now**

"We're in."

"Do you see the target?"

"He has just left the building."

"Don't let him escape!"

"We won't."

The target was a man who had just got out of a deserted-looking building. The night was too dark to reveal any of his features, he was nothing but a shadow against the wall, sliding along cautiously, as if he suspected that someone might be following. But he hadn't noticed the two black silhouettes following him from a distance, nor the other two ones watching him from a car. He was too happy for managing to get what he came after, a computer virus which his boss had wanted to get for a long time, the virus which would bring his freedom. He has been a thief for as long as he remembered, even when he was a child which should have had better things to do than sneak inside abandoned buildings at night to get some precious item sought by his boss. He was happy with his life for the simple fact that he had never known of anything better.

As he was getting closer to the crowded streets of the city he forced himself to act more naturally. He looked one last time behind him to make sure everything was safe when to his great surprise he noticed he was followed. With just one glance he noticed the essential details: two of them, man and woman.

He was hurrying up into the crowd when his phone rang.

"Hello, Phoebus" he heard a feminine voice speak.

"Who..." he started asking, but he didn't get a chance to finish his sentence:

"Who I am is hard to explain right now and you don't have the time. You have noticed my crew is following you. You don't need to be scared, they're here to protect you. Look at your right, but don't make it too obvious"

Phoebus took a quick glance while the voice on the phone continued to explain.

"Of course you notice the black car that's also been keeping a close eye on you. It's them you need to fear, it's them you need to run away from, right now. Your life is in great danger. I'll see you on the other side".

Phoebus was surprised but at the same time undecided.

"_What the...? Who was that? Now what do I do? If I don't deliver this in time my boss will kill me... If I stick around, probably one of these other guys would do the same. Well, there's only one thing a normal person would do in such a situation..."_

He stopped for a few moments and looked around for the opportunity to put his idea into practice. On the other side of the street he noticed a car pull over and the driver about to get out. Ignoring the relatively heavy traffic he ran across to the other side and before anyone could realize, he pushed the driver aside and stole the car, driving away.

"What is he doing, is he crazy?"

"He must be. I wonder how come they're not following"

"They're not but we'll be" spoke one of the two mystery followers, a young woman. She and the man that was accompanying her rushed to a nearby alley where their motorcycles were parked. In a matter of seconds they were on the trail of their target.

Meanwhile, Phoebus drove away wishing to get out of town as fast as possible. He had never been out of town, he had no idea where he'd go, he just knew that getting out of town would mean he'd be safe from everyone who was following him.

But soon he noticed he wasn't completely safe, as the man and woman were following him on two motorcycles. He drove faster looking at the sings that indicated the distance towards the city limits.

"_50 miles... 40 miles...30 miles...20 miles...10 miles...5 miles...1 mile" _he counted the distance to himself. _"I'm almost out"_ he thought when a green light suddenly appeared in front of his eyes. Blinded by the intensity of the light he almost lost control of the car.

"_Where did that guy learn to drive, I almost crashed because of him. Now let's see... What the...? Buildings, sky-skyscrapers? At the outskirts of town? Not the sight I was expecting... What?" _he thought as he hit the breaks, stopping under a traffic sign that pointed the direction towards downtown.

"_Downtown, I just got out of town 5 minutes ago, I have no idea what's this, but I know I don't like it."_

"Just when I was thinking it can't get any worst" he burst out loud, seeing his two "shadows" unmounting their motorcycles.

"Welcome back to town Phoebus. I'm sure you've enjoyed your trip out of town" the woman spoke in an ironical voice.

"Was it you guys behind...behind whatever just happened?"

"No Phoebus, you have just been a witness of what happens when you try to bend the rules of the system. You see, Phoebus, you wanted to get out of the city, there is no such place. This city is the entire world." she continued to explain.

"Nonsense. I've learned enough geography to know better" Phoebus replied with his usual cutting sarcasm.

"Have you really, or were you made think there is more? How often have you gotten out of town? How many people do you know that have?"

Phoebus looked down towards the ground and didn't reply.

"Just as I thought" she continued. "You will understand more of this later, if you come with us to save yourself. You're no longer safe here"

"Where are we going" Phoebus asked in a voice which still betrayed the lack of confidence he had for the two strangers in front of him.

"To the other side, like the Captain said, to the real world. But we must hurry" the man spoke handing Phoebus a motorcycle helmet.


	3. The Rabit Hole

**Chapter 3: The Rabithole**

Phoebus was pretty surprised to see the place where the two strangers have taken him to. It was the exact abandoned warehouse from which he had sneaked out not more than one hour behind.

"Looks familiar, doesn't it?" the man asked him. "Now, before we proceed, if you'd be so kind as to return us what you've taken from us earlier. Don't look so surprised Phoebus, we know everything about it. And I guess I'm not wrong to say you actually have no idea what you took and why you took it" the man spoke. 

Phoebus nodded and hesitated with his hand in the pocket. During these moments of silence the three had the chance to observe each other better in the dim light of the warehouse. Both Phoebus and the two strangers were surprised to see each other. Phoebus had expected to see two more mature persons, but instead he saw a man and a woman in their early twenties, around the same age as his. They had expected Phoebus to be quite different as well. Judging by what they knew about his occupation, they were expecting him to be more of a common thief with no conscience, but instead they were looking at a young man who could quite easily be mistaken for a kid.

After these moments of silence Phoebus finally took a decision. He withdrew his hand from the pocket of his brown coat holding a small parcel which he handed to the young woman.

"So that's what all the hot fuzz was for? This ... thing?" Phoebus asked.

"This thing as you call it, Phoebus,is a small something that will make a huge difference for the future. But you'll understand more about it later. Now you need to know why we came for you. Are you ready?" the man asked.

"Why not... go ahead, speak up" Phoebus spoke trying to hide his emotion.

"Phoebus, have you ever heard of The Matrix?" the man begin speaking. 

But Phoebus couldn't hear him. The mere hearing of the word "The Matrix" caused such an impression to him that he felt as if he had been hit on the head. The building seemed to be moving around him as he lost his balance and fell on his knees. He could hear a voice continuing to speak:

"_What you see is not real, it's all a dream, an illusion created by computers. This is not the real world, you must wake up...wake up...wake up...wake up..._"

These last words echoed through his brain like the sound of thunder. He was feeling the worst headache he had ever had in his life, he felt as if his head was about to explode.

"Phoebus, what's wrong, are you OK?" the woman asked him trying to help him lay on his back.

"Operator, something is wrong... What do you mean? No, we didn't get the chance to..." the man was shouting into a phone.

The young woman had pulled out some equipment which had been carefully hidden behind stacks of boxes, and was now connecting Phoebus to check his vital signs. Meanwhile Phoebus' face was grimacing from pain. As the voice still continued to echo in his head, he fixed his eyes on the dim light, trying to focus away from the pain. But he didn't manage to, as the light was now growing more and more powerful, turning red, separating into two red lights, two eyes looking into his own. Phoebus tried closing his eyes to chase the illusion away.

"Michael, come see this" the woman spoke in a very worried voice. As he stopped his conversation on the phone and approached she continued. "Look at the values. How can it possibly be? It looks like he's..."

"Quick, we need to rush" Michael spoke while dialing a number on his cell phone. "Operator, be ready. Have you traced him? ... Something is really wrong ... OK, be ready to get us out too"

"Jess, get ready, we have to go now"

"But what about him?" she asked.

"He'll be fine. We'll see him on the other side"

After Phoebus closed his eyes, he hadn't met the darkness which he would have expected. The red lights weren't there any more, but now a powerful white neon light was shining right above him. He was feeling cold. He tried to move but he couldn't, he was too weak. He felt himself rising through the air, closer to the light. The motion and his weak state made him faint. 

When he opened his eyes, he found himself lying down, surrounded by people whose faces he couldn't see as the lights were shining behind them. He only found the force to ask where he was.

"You're on the other side. Welcome to the real world" he heard a woman reply to him before losing his conscience.


	4. The Mess Hall

_Here is the new chapter. It took me quite a while to complete it, as I'm not really a fan of writing these "background story" chapters. _

_However hope you enjoy reading, and review if you have anything to say_**  
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**Chapter 4: The Mess Hall**

The Sapientia had a small mess hall, just like all the other hovercrafts, but the crew still considered it the best place on the entire ship. After a tiring day, there was nothing they liked better than gathering around the small metal table and talking about all types of random things, just to get their minds off the problems they had faced.

The mess hall looked even smaller with four serious looking persons sitting around the metal table. They spoke in a low voice, as if they feared they might be heard.

"Jess, Michael, what happened out there? I've never seen such a thing" Sirius, the operator asked. He was a young man, just like the rest of the crew, The Sapientia was the first ship where he was in charge of communications, yet they all trusted him no matter what, as he had been trained by Link.

Jessie and Michael were the center of attention. At the age of 23, they had already participated in over one hundred missions. They were considered a "rare phenomenon" as, in the history of Zion, not many pair of twins have been discovered to exist in the machine power plant. They had been freed at only 16 years, and by the age of 18 they were already been fully trained and chosen to join the crew of The Sapientia.

The fourth person in the room was Orion, the man in charge with the mechanics on the ship. He was the oldest of the crew members though he had only turned 35 that year. He was also the most silent member of the crew, he could rarely be heard speaking with anyone, and when he did speak, it was usually on matters concerning the well-functioning of the hovercraft. Though he had his own questions about the events that took place that night, he allowed Sirius to be the one to ask Jessie and Michael about them.

"We don't know either" Jessie replied to Sirius.

"You've seen just as much as we did and we know just as much as you. As soon as I mentioned the Matrix he collapsed and the next thing we know, his vital signs go crazy and he's out" Michael continued.

"That's what I don't understand: how can he be out, standing there, recovering, if he hasn't taken the pill?" Sirius spoke in a low voice, more to himself than to the others. 

"It was self-substantiation"

The reply made everyone turn their head towards the door, where Selene, the captain was standing. They didn't know she had been there, nor for how long, but now they all felt as if they had been doing something wrong in discussing what happened to Phoebus.

Selene was known as one of the best captains, despite the fact that she was the youngest. She was only twelve when she was given the chance to free herself from the Matrix. Later on, she was told that persons that young were rarely given the red pill, but in her case, The Oracle insisted that she should be found and awaken to reality.

She had chosen to be trained as a soldier and had proved to be very skilled. Most of the older red pills were impressed by her ability to drive a ship in the real world, and to fight inside the Matrix. When she confronted agents, she would always defeat them and escape without a scratch. This is why she was often compared with Neo. But she didn't know too much about Neo. She knew that he was The One, that he brought peace between men and machines, and that he died the year she was born. But she also knew that the peace he had managed to obtain at the cost of his life did not last for long. The machines were trying to destroy Zion once more, while the free humans were trying to find a way to destroy the machines.

At 20 years, Selene was offered her own hovercraft, the rank of captain, and she was asked to find herself a crew and go out to help free humans from the Matrix. She had picked ten people...during five years only four of them have survived. This was part of the reason why she had changed so much. She used to be a very optimistic and happy person, she was very friendly to all of her crew, Jessie always thought of her as a sister, but with each crew member that would die in mission, she would become more and more silent, closed within her own world, as she would blame herself for not being able to take better care of her people.

The other part of the reason was a visit she made to the Oracle soon after she took over the command of The Sapientia. She never spoke too much about what had happened there, but it was obvious for everyone that the Selene that came out of the Oracle's house was not the same Selene that had entered. She only told her crew about the mission that was assigned to their ship: locating fragments of a program that would help destroy the Matrix. There were 25 fragments. She had managed to find 20 of them. The 21st was the one Phoebus had stolen a few hours before being freed. 

Jessie was the first one that dared brake the awkward silence:

"Self-substantiation? I thought it was just a myth"

"No, it's not. It does exist, but it rarely happens. Sometimes a person manages to become aware of the Matrix, to feel it, to know it's fake, and they manage to wake up through their own will. But in all the recorded cases, the persons who have been through it had previous information about the Matrix, they had small doubts about the world they lived in, more or less confirmed by our people. As for Phoebus, our records don't show that he might have ever heard about it, that he ever had any doubts and questions" Selene explained as everyone listened in amazement.

"Then how did he did he manage to..." Jessie wanted to ask, but Selene didn't let her finish:

"That's what we don't know and what we need to find out. Now everyone back to their position. Jessie and Michael, you two are in charge of Phoebus, get him on his feet fast".

Selene left the mess hall and headed for her room. She felt like slamming the door behind her, but she had to fight her impulse as it might have drawn too much unwanted attention from everyone on the ship.

"_OK Selene, relax! Just because the guy went trough self-substantiation doesn't make him any different... There's nothing to worry about, it can't be him. Relax..."_

A knock on the door interrupted her thoughts. She opened it to find Jessie in the doorstep, looking really worried.

"Se...I'm sorry, Captain, we need you to come quick, something appears to be wrong with Phoebus"


End file.
